Recent discoveries have revealed a broad class of sequence motifs located in the 5' untranslated region of bacterial mRNAs that have the ability to regulate gene expression at the level of either transcription or translation in response to intracellular metabolite concentrations. These RNA elements, dubbed riboswitches, are able to directly effect gene regulation by binding a small molecule (guanine, lysine or thiamine pyrophosphate, for example). In B. subtilis, these RNA elements appear to control the proper expression of at least 2% of all genes, suggesting that they are a fundamentally important regulatory mechanism within the cell. To understand how these elements control gene expression crystals of a guanine riboswitch-ligand complex that diffract X-rays to at least 2.9 A resolution have been obtained. Using X-ray crystallography, this structure, along with the related adenine-responsive element will be determined to define the features of the RNA that contribute to the high affinity and specificity of ligand binding which will lead to a general understanding of how gene regulation can be effected by metabolites. In parallel, the energetics of ligand recognition will be probed using isothermal calorimetry (ITC) and a series of RNAs that contain functional group deletions.
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